NGLVieweR: Create a NGLVieweR

In NGLVieweR: Interactive 3D Visualization of Molecular Structures

Description

NGLVieweR can be used to visualize and interact with Protein Data Bank (PDB) and structural files in R and Shiny applications. It includes a set of API functions to manipulate the viewer after creation in Shiny.

Usage

NGLVieweR(data, format = NULL, width = NULL, height = NULL, elementId = NULL)

Arguments

data	PDB file or PDB entry code
format	Input format (.mmcif, .cif, .mcif, .pdb, .ent, .pqr, .gro, .sdf, .sd, .mol2, .mmtf). Needed when no file extension is provided.
width, height	Must be a valid CSS unit (like '100%', '400px', 'auto') or a number, which will be coerced to a string and have 'px' appended.
elementId	optional element Id

Details

The package is based on the NGL.js JavaScript library. To see the full set of features please read the official manual of NGL.js.

Value

A NGLVieweR htmlwidgets object.

See Also

• NGLVieweR_proxy() for handling of API calls after rendering.

• NGLVieweR_example() See example "API" and "basic".

Examples

# Example 1: Most Basic
NGLVieweR("7CID") %>%
 addRepresentation("cartoon", param = list(name = "cartoon", colorScheme="residueindex"))

# Example 2: Advanced
NGLVieweR("7CID") %>%
  stageParameters(backgroundColor = "white") %>%
  setQuality("high") %>%
  setSpin(FALSE) %>%
  addRepresentation("cartoon",
    param = list(
      name = "cartoon",
      colorScheme = "residueindex"
    )
  ) %>%
  addRepresentation("ball+stick",
    param = list(
      name = "ball+stick",
      colorValue = "red",
      colorScheme = "element",
      sele = "200"
    )
  ) %>%
  addRepresentation("label",
    param = list(
      name = "label", sele = "200:A.O",
      showBackground = TRUE,
      backgroundColor = "black",
      backgroundMargin = 2,
      backgroundOpacity = 0.5,
      showBorder = TRUE,
      colorValue = "white"
    )
  ) %>%
  addRepresentation("surface",
    param = list(
      name = "surface",
      colorValue = "white",
      opacity = 0.1
    )
  ) %>%
  zoomMove("200", "200", 2000, -20)

#---------------------Using Shiny-------------------------

# App 1: Basic Example
if (interactive()) {
  library(shiny)
  ui <- fluidPage(NGLVieweROutput("structure"))
  server <- function(input, output) {
    output$structure <- renderNGLVieweR({
      NGLVieweR("7CID") %>%
        addRepresentation("cartoon",
          param = list(
            name = "cartoon",
            colorScheme = "residueindex"
          )
        ) %>%
        addRepresentation("ball+stick",
          param = list(
            name = "cartoon",
            sele = "1-20",
            colorScheme = "element"
          )
        ) %>%
        stageParameters(backgroundColor = "black") %>%
        setQuality("high") %>%
        setFocus(0) %>%
        setSpin(TRUE)
    })
  }
  shinyApp(ui, server)
}

# App 2: Example with API calls
if (interactive()) {
library(shiny)

ui <- fluidPage(
  titlePanel("Viewer with API inputs"),
  sidebarLayout(
    sidebarPanel(
      textInput("selection", "Selection", "1-20"),
      selectInput("type", "Type", c("ball+stick", "cartoon", "backbone")),
      selectInput("color", "Color", c("orange", "grey", "white")),
      actionButton("add", "Add"),
      actionButton("remove", "Remove")
    ),
    mainPanel(
      NGLVieweROutput("structure")
    )
  )
)
server <- function(input, output) {
  output$structure <- renderNGLVieweR({
    NGLVieweR("7CID") %>%
      addRepresentation("cartoon",
        param = list(name = "cartoon", colorScheme = "residueindex")
      ) %>%
      stageParameters(backgroundColor = input$backgroundColor) %>%
      setQuality("high") %>%
      setFocus(0) %>%
      setSpin(TRUE)
  })
  observeEvent(input$add, {
    NGLVieweR_proxy("structure") %>%
      addSelection(isolate(input$type),
        param =
          list(
            name = "sel1",
            sele = isolate(input$selection),
            colorValue = isolate(input$color)
          )
      )
  })

  observeEvent(input$remove, {
    NGLVieweR_proxy("structure") %>%
      removeSelection("sel1")
  })
}
shinyApp(ui, server)
}

NGLVieweR documentation built on June 1, 2021, 9:08 a.m.